Near the end of chapter 7, Jem and Scout are on the way to school when Jem notices that "someone had filled [their] knot-hole with cement." So, the hole where the mysterious friend had been leaving gifts for Scout and Jem was completely filled in with cement. Jem immediately tries to reassure Scout, telling her not to cry. But then he gets to thinking, and starts watching for Mr. Radley to walk by. As soon as he does, Jem asked him if he was the one to fill that tree hole with cement. Mr. Radley confirms that it was, and the reason was that the "tree's dying. You plug 'em with cement when they're sick." Well, this explanation doesn't sit well with Jem. He asks Atticus if the tree is sick, and Atticus confirms that it is a very healthy tree. Then, Jem stays out on the porch, upset, and when he comes in, Scout "saw that he had been crying."
All of this implies that Boo was leaving things for the children, and Mr. Radley, who Calpernia in chapter one said was "the meanest man ever God blew breath into", filled the hole with cement to put a stop to their friendship. It is a very sad thing, Boo's father shutting down any sort of happiness or companionship, and Jem is obviously upset that he would be so mean to his own son.
The cement hole is filled by Nathan Radley and the reason he said he filled it was because the tree was dying when in fact it was not. When Jem talks to Atticus about it he says the tree was healthy. Jem was upset because he liked making a new friend and receiving gifts, and this meant that this would end.
The knot-hole was filled with cement by Mr. Nathan Radley. Mr. Radley said he filled it in because the tree was dying, but when Jem asks Atticus about it, Atticus says the tree looked healthy to him. Jem was extremely upset about the tree, and cries on the porch about it, because it meant the end of the children's relationship with whomever was leaving the gifts.